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Hongan Long
Postdoctoral Researcher

Ph.D., 2012, Biology, University of Houston

M.S., 2007, Marine Biology, Ocean University of China

B.S., 2004, Bioscience, Ocean University of China

I study the rate and molecular spectrum of mutations arising in microbial species, exposed to both natural background environments and to potential environmental mutagens such as sublethal concentrations of antibiotics/herbicides/pesticides.

Mutation is the ultimate source of genetic variation. However, mutations are notoriously hard to catch, because of their rarity and easy loss due to purifying selection. Mutation accumulation procedures conquer these difficulties by setting up large number of replicate cell lines from a single cell ancestor and single-cell/colony transfers on rich media to maximize genetic drift. Most studies on spontaneous mutations were based on indirect methods to derive mutation rates, for example, synonymous site or pseudogene mutation rate through DNA sequence comparison between different organisms, reporter construct based on only one or a handful genes, or fitness assays on mutation accumulation lines. Since 2008, when whole-genome sequencing began to be commercially available, the Lynch lab started directly detecting spontaneous mutations by deeply sequencing the mutation accumulation lines. I am currently reaching out to environmental mutagenesis using mutation accumulation techniques combined with whole-genome sequencing (MA/WGS).

My post-doc research focuses on:

  1. Explore spontaneous mutation rates and spectra of unicellular microbes, including bacteria and eukaryotes, broadly sampled from the Tree of Life, as well as factors influencing mutation rates. Up to date, the findings are: mutations are not random, mutation rate of a single nucleotide is influenced by the flanking nucleotide and the genomic position; there are exceptions of the “universal A/T bias” of bacteria, and mutation types of an organism could be highly variable and influenced by the biology and the outside environment, though mutation rate per genome per generation does not vary much; unicellular eukaryotes do have lower mutation rate than other microbes, with ciliated protozoa as extremely low cases; DNA mismatch repair is biased in repairing different types of mutations, etc.
  2. Apply mutation accumulation/whole-genome sequencing (MA/WGS) method to studies on mutagenic effects of long-term pollutant exposure. For this part, I am trying to answer: how low levels of antibiotics cause mutations and what kind of mutations are induced during antibiotics treatments in the model bacterium E. coli K-12 MG1655; whether mutator strains have higher chances of gaining resistance; are there any indications of oxidative mutations derived from antibiotic treatment? I am also expanding this kind of environment induced mutations to pathogenic bacteria like Salmonella enterica, Staphylococcus aureus etc., as well as yeasts Saccharomyces cerevisiae, Candida albicans.

Undergraduate Research Assistants

Proudly as a person born in Wenshang, Shandong Province, China, which was under governing of Confucius (ancient educationist and philosopher of China; he was the mayor of Zhongdu for one year-500 B.C.; Zhongdu was the ancient name of Wenshang), I am eager to contribute to college/graduate education in Biology. I feel very lucky to practise some of my teaching/training ideas on my undergraduate research assistants, who are excellent undergraduate students in Department of Biology, IU.

Many of my projects could not be finished if without help from my undergradute research assistants. They, like mirrors, help me improve my teaching/research/language skills, and I am more than happy to do anything to boost their long-term career. I am very proud of these guys and wish the best of them no matter where they will land: Hongan's awesome undergraduate researchers that have worked or are working in the Lynch lab.

Selected Publications

Long, H., Miller, S., Strauss, C., Zhao, C., Cheng, L., Ye, Z., Griffin, K., Te, R., Lee, H., Chen, C., Lynch, M. 2016 Antibiotic treatment enhances the genome-wide mutation rate of target cells. Proceedings of National Academy of Sciences, USA 113(18): E2498-E2505.

Farlow1, A., Long1, H., Arnoux, S., Sung, W., Doak, T., Nordborg, M., Lynch, M. 2015.The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe. Genetics 201(2):737-44. (1 co-first author)

.Xu, S., Ackerman, M., Long, H., Bright, L., Spitze, K., Ramsdell, J.S., Thomas, W.K., Lynch, M. 2015. A male-specific genetic map of the microcrustacean Daphnia pulex based on single sperm whole-genome sequencing. Genetics 201(1):31-38.

Long1, H., Kucukyildirim1, S., Sung, W., Williams, E., Lee, H., Ackerman, M., Doak, T.G., Tang, H., Lynch, M. 2015. Background mutational features of the radiation-resistant bacterium Deinococcus radiodurans. Molecular Biology and Evolution. 32(9): 2383-2392. (1 co-first author)

Long, H., Sung, W., Miller, S., Ackerman, M., Doak, T., Lynch, M. 2015. Mutation rate, spectrum, topology and context dependency in the DNA mismatch repair deficient Pseudomonas fluorescens. Genome Biology and Evolution 7(1): 262-271.

Long, H., Zufall, R. 2015. Mutational robustness of morphological traits in the ciliate Tetrahymena thermophila. Journal of Eukaryotic Microbiology 62(2): 249-254.

Long, H., Paixao, T., Azevedo, RBR, Zufall, RA. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics 195: 527-540

Long, H., Zufall, RA. 2010. Diverse modes of reproduction in the marine free-living ciliate Glauconema trihymene. BMC Microbiology. 10: 108. 

Long, H., Liu, H., Liu, W., et al. 2008. Two new ciliates from Hong Kong coastal water: Orthodonella sinica n. sp. and Apokeronopsis wrighti n. sp. (Protozoa: Ciliophora). Journal of Eukaryotic Microbiology. 55: 321-330;

Long, H., Song, W., Wang, Y. and Li, J. 2007. Morphological redescription of two endocommensal ciliates, Entorhipidium fukuii Uyemura, 1934 and Madsenia indomita (Madsen, 1931) Kahl, 1934 from digestive tracts of sea urchins of the Yellow Sea, China (Ciliophora; Scuticociliatida). European Journal of Protistology. 43: 101-114;

Long, H., Song, W., Chen, J., et al. 2006. Studies on an endoparasitic ciliate Boveria labialis (Protozoa: Ciliophora) from the sea cucumber, Apostichopus japonicus. Journal of Marine Biological Association, U. K. 86: 823-828.

Long, H. 2000. A useful solid geometry function. Mathematics and Physics World (High School Edition, in Chinese). 71: 42.